Bluepymm

A new required conf field was added to the prepare step: 'rep_morph_path'.
This has to point to a morphology release with repaired morphologies, and this directory has to contain the repaired versions of all the exemplar morphologies. The old 'morp_path' still exists, and points to the morphology release directory used for circuit building. The latter doesn't need to include the repaired exemplar morphologies though.

The conf file of the select doesn't accept the key 'mm_run_path' anymore, this is replaced with e.g.:
"scores_db": "./output/scores.sqlite"

We removed the bluepymm-megate command, and everything now goes through the 'bluepymm' command.
It now acts a bit like the 'pip' command, with subcommands.

There are three stages:
prepare, run and select

'bluepymm prepare <configfile>' builds the me-combo database from the input files
'bluepymm run <configfile>' takes the database and runs all the combos
'bluepymm select <configfile>' is the megating step

A sample of a config for the new 'run' phase is here:
https://github.com/BlueBrain/BluePyMM/blob/master/bluepymm/tests/examples/simple1/simple1_conf_run.json

The bluepymm command will show an help message if you run it without argument.